title: Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics.
abstract: Mass-spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. Here we describe a new module integrated into PatternLab for Proteomics that allows the pinpointing of differentially expressed domains. This is accomplished by inferring functional domains through our cloud service, using HMMER3 and Pfam remotely, and then mapping the quantitation values into domains for downstream analysis. In all, spotting which functional domains are changing when comparing biological states serves as a complementary approach to facilitate the understanding of a system's biology. We exemplify the new module's use by reanalyzing a previously published MudPIT dataset of Cryptococcus gattii cultivated under iron-depleted and replete conditions. We show how the differential analysis of functional domains can facilitate the interpretation of proteomic data by providing further valuable insight.
authors.affiliation: Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Paraná, Brazil.
authors.forename: F V
authors.initials: FV
authors.lastname: Leprevost
authors.forename: D B
authors.initials: DB
authors.lastname: Lima
authors.forename: J
authors.initials: J
authors.lastname: Crestani
authors.forename: Y
authors.initials: Y
authors.lastname: Perez-Riverol
authors.forename: N
authors.initials: N
authors.lastname: Zanchin
authors.forename: V C
authors.initials: VC
authors.lastname: Barbosa
authors.forename: P C
authors.initials: PC
authors.lastname: Carvalho
mesh_terms: D056285:Cryptococcus gattii / Q000737:chemistry* / Q000378:metabolism*; D030562:Databases, Protein; D005656:Fungal Proteins / Q000096:biosynthesis / Q000737:chemistry; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000096:biosynthesis / Q000737:chemistry; D040901:Proteomics / Q000379:methods*
chemical_list: D005656:Fungal Proteins; D020543:Proteome
keywords: Bioinformatics; Computational proteomics; Functional analysis; Protein domains; Proteomics